title: Anatomical Site-Specific Carbohydrate Availability Impacts Streptococcus pneumoniae Virulence and Fitness during Colonization and Disease

city: Baltimore

first: Suvarna

last: Nadendla

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Transcriptomic analysis of Streptococcus pneumoniae TIGR4 wildtype and it's isogenic ccpA mutant, grown in chemically defined media supplemented with physiological levels of carbohydrates to mimic the human nasopharynx and bloodstream. The goal is to examine how anatomical site-specific carbohydrate availability impacts S. pneumoniae physiology and virulence.

overall_design:
6 mRNA profiles of Streptococcus pneumoniae wildtype and ccpA mutant samples that were grown in chemically defined media supplemented with physiological levels of carbohydrates to mimic the human nasopharynx and bloodstream. BioProject: PRJNA781242
Funding Source: This work was supported by NIH National Institute of Allergy and Infectious Diseases (NIAID) grants AI148368, AI114800, AI156898, and AI146149 to C.J.O. and AI146149 to H.T. H.I. is supported by NIH grant T32 HL129948. The High-Field NMR facility at the University of Alabama at Birmingham was established through NIH grant S10RR026478 and is currently supported through the comprehensive cancer center (NCI grant P30 CA013148).

first: Hansol

last: Im

first: Katherine

middle: L

last: Kruckow

first: Adonis

last: D’Mello

first: Feroze

last: Ganaie

first: Eriel

last: Martinez

first: Jennifer

last: Luck

first: Kyle

last: Cichos

first: Ashleigh

last: Riegler

first: Xiuhong

last: Song

first: Elie

last: Ghanem

first: Jamil

last: Saad

first: Moon

last: Nahm

first: Herve

last: Tettelin

first: Carlos

last: Orihuela


title: IL-10 Signaling Restricts Murine Progenitor Cell Expansion and Preserves Stem Cell Function

status: Public on Nov 19 2021

city: Boston

first: David

middle: Allan

last: Williams

state: MA

address: 300 Longwood Ave.

department: Hematology/Oncology

country: USA

institute: Boston Children's Hospital

type: Expression profiling by high throughput sequencing

summary: Inflammation causes increased signaling and proliferation in hematopoietic stem and progenitor cells (HSPCs), but the specific role of anti-inflammatory cytokines such as IL-10 on HSPCs is less clear. Using IL-10 receptor (IL-10R)-deficient mice we observed an increased frequency and number of HSPCs in the bone marrow (BM) relative to wild-type (WT) mice with an increased frequency of mature myeloid cells. Consistent with this, we observed reduced expansion of WT lineage-negative HSPCs after in vitro exposure to IL-10 with a specifically pronounced suppression of MPP2 cells. This reduced expansion was not observed with IL-22 or IFN-λ2, cytokines which signal through receptors that also contain the IL-10 receptor common β chain or with HSPCs from Il10ra-/- mice. To understand the mechanism of reduced expansion of MPP2 cells and preserved HSC numbers in mice with intact IL-10 signaling, we stimulated FACS-purified WT cells with IL-10 and performed expression analysis. IL-10 stimulation of HSCs increased the non-canonical Wnt pathway gene Wnt4 which is implicated in HSC quiescence and long-term function. In contrast, IL-10 stimulation in MPP2 cells modulated the TGFβ pathway and increased the expression of E2f5, a transcription factor that negatively regulates proliferation. Taken together, this study reveals a previously unrecognized role for IL-10 in suppressing HSPC cell expansion and promoting HSC function.

overall_design: mRNA profiles of MPP2 and LT-HSC cells after stimulation with IL-10

middle: A

first: Kurt

last: Whittemore


title: Analysis of liver sinusoidal endothelial cells (LSECs) with β-catenin (Ctnnb1) activation

status: Public on Nov 18 2021

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

summary:
Endothelial-derived Wnt/Ctnnb1-signaling is an important angiocrine regulator. Ctnnb1 gain-of-function (GOF) in liver sinusoidal endothelial cells was generated by crossing Clec4g-iCre (Wohlfeil SA et al, 2019, Cancer Research) with Ctnnb1(Ex3) fl/fl mice (Harada N et al, 1999, EMBO J) to analyze the effects of endothelial β-catenin signaling on LSEC differentiation and liver function
We used microarrays to detail the global programme of gene expression in liver sinusoidal endothelial cells with β-catenin (Ctnnb1) gain-of-function compared to control animals.

overall_design: Mice (female) aged 2 months (Control, Ctnnb1OE-EC) were sacrificed, the liver was perfused and liver sinusoidal endothelial cells were isolated using CD146 magnetic beads. RNA was isolated immediately afterwards and prepared for microarray analysis.

first: Victor

last: Olsavszky


title: Protection against autoimmunity is driven by thymic epithelial cell-mediated regulation of Treg development

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: Thymic education of Tregs is superior to negative selection in the prevention of autoimmunity. To address this hypothesis, TCR repertoirs of thymic and peripheral Tcells (including Tregs) from conditional NIK KO and WT mice have been sequenced and compared.

overall_design: conventional CD8, CD4 T cells and Tregs cells have been sorted from thymus, spleen and lung of 3 WT and 3 Foxn1CrexNIKflfl mice. The analysis is based on the sequecing of the respective TCRb RNAs

first: Claudia

last: Haftmann

first: Florian

last: Ingelfinger

first: Pascale

last: Zwicky

last: Mair

first: Stefan

last: Flöss

first: Rene

last: Riedel

first: Marianne

last: Spalinger

first: Ekatarina

last: Friebel

first: Brian

last: Leung

first: Jan

last: Kieslow

first: Ari

last: Waisman

first: Mir-Farzin

last: Mashreghi

first: Jochen

last: Hühn

first: Burkhard

last: Becher


title: Epigenome analysis of gliomas with EWSR1-BEND2 fusions

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

summary: Genome-wide DNA methylation profiling of 4 gliomas with EWSR1-BEND fusions with histologic features resembling astroblastoma. The Illumina Infinium EPIC 850k Human DNA Methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpG sites of genomic DNA extracted from formalin-fixed, paraffin-embedded tumor tissue of 4 gliomas with EWSR1-BEND2 fusions.

overall_design: Bisulfite converted genomic DNA extracted from the 4 tumor samples was hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchip


title: Specificity of ADAR1-isoforms: RIP-seq of ADAR1p150 and ADAR1p110 in HEK293 cells

city: Vienna

first: Renata

last: Kleinova

address: Schwarzspanierstrasse 17

department: CACB

country: Austria

institute: Medical University of Vienna

summary: Adenosine deaminase acting on RNA (ADAR) (also known as ADAR1) promotes A-to-I conversion in double-stranded and highly structured RNAs. ADAR1 has two isoforms transcribed from different promoters: ADAR1p150, which is mainly cytoplasmic and interferon-inducible, and constitutively expressed ADAR1p110 that is primarily localized in the nucleus. Mutations in ADAR1 cause Aicardi – Goutières syndrome (AGS), a severe autoinflammatory disease in humans associated with aberrant IFN production. In mice, deletion of ADAR1 or selective knockout of the p150 isoform alone leads to embryonic lethality driven by overexpression of interferon-stimulated genes. This phenotype can be rescued by concurrent deletion of cytoplasmic dsRNA-sensor MDA5. These findings indicate that the interferon-inducible p150 isoform is indispensable and cannot be rescued by the ADAR1p110 isoform. Nevertheless, editing sites uniquely targeted by ADAR1p150 but also mechanisms of isoform- specificity remain elusive. To examine in vivo interaction between ADAR1-isoforms and its substrates, we performed RNA immunoprecipitation and sequencing (RIP-seq) in HEK293 cells. RIP-seq experiment was done with overexpressed flag-tagged ADAR1 isoforms.

overall_design: RIP-seq experiment with overexpressed ADAR1-isoforms was performed in HEK293 cells. ADAR1p150 and ADAR1p110 RIP-seq was done in biological triplicates and MOCK (untransfected) control in biological duplicates. For all the samples mentioned above, relevant input samples were collected and sequenced.

first: Alina

middle: F

last: Leuchtenberger

first: Michael

last: Jantsch


title: Cyclophosphamide enhances the anti-tumor potency of GITR engagement by  increasing oligoclonal cytotoxic T cell fitness

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Immune checkpoint blockade (ICB) therapy is a standard treatment option for many  malignancies, but it is only effective in a subset of patients. Combination strategies to  overcome resistance are promising areas of investigation. Targeting glucocorticoidinduced  TNFR-related (GITR) protein with agonist antibodies has shown efficacy in  preclinical models, but GITR engagement does not control growth of advanced poorly  immunogenic murine tumors such as B16 melanoma and has not yielded benefit in  clinical trials. The alkylating agent cyclophosphamide (CTX) preferentially depletes  regulatory T cells (Tregs) and expands tumor-specific effector T cells (Teffs) via  homeostatic proliferation. Additionally, CTX directly induces tumor cell death, thereby  releasing antigen to prime Teffs in a lymphopenic environment where there are fewer  Tregs. GITR agonism has a net inhibitory effect on Tregs and yet activates Teff. We  therefore hypothesized that CTX treatment prior to GITR agonism would promote potent  anti-tumor immunity. Here we show that the combination of CTX and GITR agonism  robustly controls tumor growth in several clinically relevant mouse models.  Mechanistically, we show that the combination therapy causes tumor cell death, clonal  expansion of highly active and terminally differentiated CD8+ T cells, and depletion of  regulatory T cells by AICD. Control of tumor growth was also associated with the presence  of an expanded population of highly activated tumor-infiltrating oligoclonal CD8+ T cells  that lead to a global contracted TCR repertoire. Our studies show that the combination of  CTX and GITR agonism is a rational chemo-immunotherapeutic approach that warrants  further clinical investigation.

overall_design: Single cell transcriptome and hashtaging and next geration TCR sequencing of 5 mice per condition

first: Daniel

last: Hirschhorn

first: Levi

last: Mangarin

first: Andrew

last: Chow

first: Taha

last: Merghoub


title: Fundamentals of Vaping-Associated Pulmonary Injury  Leading to Severe Respiratory Distress [Visium]

city: San Diego

first: Oscar

middle: E

last: Echeagaray

address: 5500 Campanile Drive

department: Biology

institute: San Diego State University

summary: Spatial transcriptomic (10X Genomics Visium) to profile pulmonary branches from Non-Vaped (NV) and Vaped (V) mice.

overall_design: Spatial Transcriptional profiling of  upper pulmonary brances of Non-Vaped (NV) and Vaped (V) mice by gene expression slides approach using 10X Genomics Visium Platform

first: Mark

last: Sussman

first: Carolina

last: Esquer


title: Aberrant extrafollicular B cells, immune dysfunction and myeloid inflammation precede malignancy in Waldenstrom macroglobulinemia

city: Decatur

first: Akhilesh

last: Kaushal

state: GA

address: 1760 Haygood street

institute: Emory University

summary: Waldenstrom macroglobulinemia (WM) and its precursor IgM gammopathy are distinct disorders characterized by the growth of mature IgM-expressing B cell clone predominantly in the bone marrow. Here we show that these disorders originate in the setting of expansion of genomically aberrant extrafollicular B cells, immune dysfunction and myeloid inflammation that begins before the expansion of the malignant clone. Host response to these early lesions involves the induction of tumor-specific T cell immunity that may include MYD88 mutation-specific responses. Hematopoietic progenitors carry the oncogenic MYD88 mutations characteristic of the malignant WM clone. These data provide an example of how oncogenic mutations in earlier progenitors may create the milieu promoting the evolution of malignant phenotype in differentiated cells.

overall_design: 7 bone marrow specimens each from patients with diagnosis of MGUS or Waldenstrom were obtained.4 healthy donors specimens were purchased from All Cells, Inc.. Bone marrow mononuclear cells (BMMNCs) were stained with custom panels of metal conjugated antibodies according to manufacturer-suggested concentrations (Fluidigm). Gene expression and cell surface libraries were prepared according to the protocol from 10X Genomics. Exome capture was performed using the IDT xGen v1 capture kit (Integrated DNA Technologies) according to manufacturer’s instructions. The presence of WM-specific T cells in blood or bone marrow was quantified both directly ex vivo and after in vitro stimulation with autologous tumor loaded DCs using a 16h ELISPOT assay.

first: Ajay

middle: K

last: Nooka

first: Allison

last: Carr

first: Katherine

last: Pendleton

first: Benjamin

middle: G

last: Barwick

first: Julia

last: Manalo

first: Samuel

middle: S

last: McCachren

first: Vikas

last: Gupta

first: Nisha

last: Joseph

first: Craig

middle: C

last: Hofmeister

first: Jonathan

last: Kaufman

first: Leonard

middle: T

last: Heffner

first: Stephen

middle: M

last: Ansell

first: Lawrence

middle: H

last: Boise

first: Sagar

last: Lonial

first: Kavita

last: Dhodapkar

first: Madhav

middle: V


title: Differential gene expression in oncostreams and no-oncostreams area in mouse model glioma

city: Ann Arbor

first: Maria Luisa

last: Varela

state: Michigan

address: 1150 West Medical Center Drive

department: Neurosurgery

institute: University of Michigan

summary: Our preliminary data demonstrate that malignant gliomas in both human GBM and mouse models display regular anatomical structures, ‘oncostreams’; we interpret these as a manifestation of GBM self-organization. Oncostreams’ presence correlates with tumor malignancy and parenchymal invasion.  Molecular signaling pathways that regulate oncostreams’ organization and function, however, remain unknown. We will test the hypothesis that oncostreams’ present in mouse intracranial glioma model have a characteristic transcriptome that differs from surrounding tumor, and to identify critical genes that regulate oncostreams function.

overall_design: mRNA profiles of laser microdisection samples of oncotreams and no-oncostreams areas.

first: Andrea

last: Comba

first: Pedro

last: Lowenstein


title: Transcriptome profiling of lungs in a mice model for severe COVID-19

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

summary:
For the purpose of establishing a mice model for sever COVID-19 , mice were infected intranasally with SARS-CoV-2 two days after pulmonary application of low-dose ricin.  The goal of this study is to perform a comparative transcriptomic analysis by exploring the alterations in gene expression in lungs of mice exposed to low-dose ricin and SARS-CoV-2  (samples OR009-OR012) compared to lungs of mice infected solely with SARS-CoV-2 (48 hr after infection, samples OR021-OR024) or mice exposed to low-dose ricin (96 hr post exposure,samples OR005-OR008)) or mice exposed to lethal dose of ricin (48 hr post exposure, samples OR013-OR016).
Methods: Total RNA was extracted from lungs of  ricin intoxicated mice (intranasally exposure to 1.7 µg/kg  or 10 µg/kg ricin ) or of SARS-CoV-2 infected mice (intranasal administration of 5 x 106 PFU), using the RNeasy mini kit (Qiagen). RNA-seq libraries were constructed and sequencing of 100bp paired-end was performed on the Illumina NovaSeq 6000 system. Sequencing yielded about 22M reads per sample that were mapped to the mouse genome.  RNA ratios were clustered using partitioning clustering.  We next carried out Ingenuity Pathway Analysis (IPA).
Results: Principal component analysis revealed distinct transcriptional signatures between lungs mice exposed to low-dose ricin and infected with SARS-CoV-2 compared to lungs of mice  infected solely with SARS-CoV-2 or mice exposed to low-dose ricin (96 hr post exposure) or mice exposed to lethal dose of ricin (48 hr post exposure).  Differentially Expressed Genes (DEGs) were defined as such when having false discovery rate (FDR) value (p-adjusted) of ≤ 0.01 and a fold change (FC) of ≥ 1.5 or ≤ 0.66.   Analysis of Low-dose-ricin-treated mice transcripts resulted in the detection of 6684 DEGs, 55% upregulated and 45% downregulated. Similarly, in Low-dose-ricin-treated mice infected with SARS-CoV-2, we found a total of 6044 differentially expressed genes, 52% induced and 48% repressed.  Considerably fewer (797, 67% upregulated and 33% downregulated) differentially expressed genes were identified in lungs of mice infected only with SARS-CoV-2.

overall_design: Transcriptome profiling of mice lungs exposed to low-dose ricin and/or infected with SARS-CoV-2

first: Reut

last: Falach

first: Ofir

last: Israeli

first: Galia

last: Zaide

first: Dana

last: Stein

first: Yentle

last: Ivgi

first: Moshe

last: Aftalion

first: David

last: Gur

first: Tamar

last: Sabo

first: Chanoch

last: Kronman

last: Gihon


title: "Youthful" Phenotype of c-Kit+ Cardiac Fibroblasts [DDR2_cKit]

first: Oscar

last: Echeagaray

summary: Single-cell RNA-seq (10X Genomics Chromium) to profile Adult cardiac interstitial cells sorted based on the presence of cKit, DDR2 and CD45 on cell membrane surface .

overall_design: Transcriptional profiling of  Adult cardiac interstitial cells sorted based on the presence of cKit, DDR2 or CD45 on cell membrane surface  by scRNA-Seq approaches using 10X Genomics Chromium

first: Mark

last: Sussman

first: Fareheh

last: Firouzi


title: SARS-CoV-2 infection-induced human B cells

first: Patrick

last: Wilson

address: 413 E. 69th Street

department: gale and Ira Drukier Institute for Children's Health

institute: Weill Cornell Medicine

summary: This study was designed to capture the single cell transcriptome and BCR sequence of B cells that were bait sorted using oligo-tagged viral antigens.

overall_design: Human B cells (viable/CD19+/antigen-PE+ or viable/CD19+/antigen-APC+) were bait sorted after initial magnetic enrichment and used in downstream sequencing.

first: Haley

last: Dugan

first: Christopher

last: Stamper

first: Siriruk

last: Changrob

first: Nick

middle: W

last: Asby

first: Steven

last: Erickson

first: Lei

last: Li


title: Apoptosis-associated speck-like protein containing a CARD regulates the growth of pancreatic ductal adenocarcinoma

city: Toon

first: Mitsuhito

last: Koizumi

state: Ehime

address: Shitsukawa

country: Japan

institute: Ehime University Graduate School

summary: Apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) is a key adaptor protein of inflammasomes but also a proapoptotic molecule. We clarified the role and mechanisms of ASC in vitro data based on PDAC cells. ASC expression in PDAC cells was downregulated using small-interfering (si)RNA, and gene expression was assessed by RNA sequencing. PDAC cells were further analyzed using a proliferation assay and cell cycle analysis. We observed high ASC expression in multiple PDAC cells, and downregulation of ASC resulted in inhibition of PDAC cell growth and altered expression of cell cycle-related genes. Downregulation of ASC inhibited tumor progression by modulating the cell cycle in PDAC cells.

overall_design: mRNA profiles of PANC-1 cells after transfection with either control siRNA, ASC siRNA (1), or ASC siRNA (2) were generated by deep sequencing, in triplicate, using Illumina Miseq.

first: Koizumi

last: Mitsuhito

first: Hiasa

last: Yoichi


title: Transcriptome of different cultivars of Fusarium graminearum-infected wheat grains

city: Shanghai

first: Kailin

address: Tian Ping

department: Shanghai Institute of Nutrtion and Health

country: China

institute: Chinese Academy of Sciences

summary: We report the transcriptome profile of different cultivars of Fusarium graminearum-infected wheat grains, aiming to search for some different expression genes and pathways to reveal the difference between wheat cultivars.

sample_organism:
Triticum aestivum
Fusarium graminearum

platform_organism:
Triticum aestivum
Fusarium graminearum

overall_design: Different cultivars of non-infected wheat grains and Fusarium graminearum-infected wheat grains mRNA profiles.

first: Aibo

last: Wu


title: Surf4 facilitates reprogramming by activating the cellular response to ER stress

first: Li

state: Yangpu District

address: No. 1239, Siping Road

department: School of Life and Science

institute: Tongji University

summary: By somatic cell nuclear transfer, the oocytes can reprogram terminally differentiated cells back to totipotent state. So the oocytes enriched maternal proteins attract great interests in exploring key factors in somatic cell reprogramming. Here, we presented a maternal factor, surfeit locus protein 4 (Surf4), can significantly facilitate the generation of induced pluripotent stem cells (iPSCs) in a proliferation-independent manner. When co-expressed with Oct4, Sox2, Klf4 and c-Myc (OSKM), Surf4 can activate the response to endoplasmic reticulum (ER) stress at early stage of reprogramming. Besides, blocking unfolded protein response (UPR) compromised the effect of Surf4 on reprogramming. In conclusion, Surf4 serves as an activator for somatic cell reprogramming by activating the response to ER stress.

overall_design: The reprogrammable MEFs derived from the R26rtTA Col1a14F2A Oct4EGFP mice, which harboring the doxycycline-inducible polycistronic 4F2A cassette (Oct4, Sox2, Klf4 and c-Myc), the constitutively expressed reverse tetracycline transactivator (rtTA) and expressed enhanced green fluorescent protein (EGFP) under the control of the Oct4 promoter and distal enhancer, were used in the experiments. The reprogrammable MEFs that were not induced with doxycycline were designated as “MEF”. The reprogrammable cells with or without Surf4’s overexpression were induced with doxycycline (1ug/ml) for 3 days, which were designated as “control” and “Surf4”, respectively. The cells were harvested and performed RNA sequencing (RNA-seq)

first: Wu

first: Shen

last: Jiacheng

first: Zhao

last: Kun

first: Zhang

last: Yanping


title: Shank3(∆C/+) mice exhibit altered transcriptomic response to swim stress

first: Lisa

middle: Nicole

last: Learman

state: MD

address: 725 N. Wolfe St., PCTB 917

department: Neuroscience

institute: Johns Hopkins University School of Medicine

summary: Shank3 is a postsynaptic protein that complexes with group 1 metabotropic, AMPA-, and NMDA-type glutamate receptors. Mutations of Shank3 are causal for Phelan-McDermid syndrome (PMS) and associated autism phenotypes. Individuals with PMS often exhibit sensitivity to novelty or stress that can result in behavioral deterioration. Here we use a Shank3 mouse model with face-validity to PMS [Shank(3∆C/+)] and perform a transcriptomic analysis of principal neurons from neocortex of mice subjected to brief swim stress.  Analysis reveals overrepresented pathways related to synapses accompanied by elevated expression of the immediate early gene Homer1a. In normal brain Homer1a is dynamically expressed in association with motivated behavior and mediates an essential step in sleep-related homeostatic down-scaling of synaptic proteins. This is consistent with observations that synaptic Shank3 expression requires Homer cross-linking, which is interrupted by Homer1a.  Accentuated Homer 1a expression in Shank3(∆C/+) results in marked reductions of Shank3 expression, changes in synapse composition and NMDA-dependent synaptic plasticity, and disruption of social motivation. Deletion of Homer1a partially mitigates stress-induced phenotypes in Shank3(∆C/+) mice. Homer 1a is required for developmental plasticity, learning and memory, yet its enhanced expression in Shank3(∆C/+) may underlie a vulnerability of PMS patients that highlights the challenge of clinical management.

overall_design: Pyramidal Neuron mRNA profiles of Shank3(+/+) and Shank3(∆C/+) mice on C57BL6 strain background with and without swim stress

first: Raozhou

last: Lin

middle: N

first: M

last: Bangash

first: Tatiana

last: Melnikova

first: Erica

last: Leyder

first: Nirinjini

last: Naidoo

first: David

middle: J

last: Linden

first: Joo

last: Park

first: Alena

last: Savonenko

first: Paul

last: Worley


title: In vivo gene signature of re-epithelialized tissue post-wounding from wildtype or Rnasel KO mice

first: Luis

middle: Andres

last: Garza

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

summary:
Mammalian injury responses are characterized by fibrosis and scarring rather than the functional regeneration observed in other phyla. Limited regenerative capacity in mammals could reflect a loss of pro-regeneration programs or active suppression by genes functioning akin to tumor suppressors. To uncover programs governing regeneration in mammals, we investigated Wound Induced Hair Neogenesis (WIHN), a rare example of regeneration in adult mammals1,2. Through comprehensive screening of transcripts associated with both WIHN and human facial rejuvenation after laser treatment, we found the endoribonuclease RNase L to be a powerful suppressor of regeneration. Rnasel-/- mice exhibit remarkable regenerative capacity and accelerated wound healing following injury through the production of IL-36α. Consistent with the known role of RNase L to stimulate caspase-1 signaling, we find that pharmacologic inhibition of caspases promotes regeneration in an IL-36-dependent manner. These responses are not limited to skin but occur following intestinal injury as well, suggesting that suppression of regeneration is a general characteristic of mammalian wound healing. Taken together, this work suggests a therapeutic strategy to uncover latent regenerative capacity and promote functional response to injury.
Biopsies of re-epithelialized tissue were recovered from wild-type or Rnasel KO mice approximately 10 days after wounding. Total RNA was extracted and sent for microarray analysis.

overall_design: Deep tissue wounds of 1.25cm^2 were performed on wild-type or Rnasel KO mice. After 10 days the scab detached (SD0), signifying re-epithelialization. SD0 tissue was surgically removed and total RNA was extracted and submitted for microarray analysis. A single KO sample was compared to a single WT sample.


title: Essential role of JAB1 in  human chondrosarcoma pathogenesis

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: RNA sequencing was performed at the Genomics Core - Case Western Reserve University

overall_design: Three WT controls and three JAB1-shRNA knockdown human chondrosarcoma, SW1353, samples were analyzed for RNA-sequencing analysis.

first: Murali

last: Mamidi

first: William

last: Samsa

first: Alex

last: Miron

first: E

first: Guang

last: Zhou


title: Enteric coronavirus infection and treatment modeled with an immunocompetent human intestine-on-a-chip

status: Public on Nov 17 2021

city: Cambridge

first: Vincent

middle: Nevan

last: Miao

state: Massachusetts

address: 400 Main St.

institute: MIT

summary: Many patients infected with coronaviruses, such as SARS-CoV-2 and NL63 that use ACE2 receptors to infect cells, exhibit gastrointestinal symptoms and viral proteins are found in the human gastrointestinal tract, yet little is known about the inflammatory and pathological effects of coronavirus infection on the human intestine. Here, we used a human intestine-on-a-chip (Intestine Chip) microfluidic culture device lined by patient organoid-derived intestinal epithelium interfaced with human vascular endothelium to study host cellular and inflammatory responses to infection with NL63 coronavirus. These organoid-derived intestinal epithelial cells dramatically increased their ACE2 protein levels when cultured under flow in the presence of peristalsis-like mechanical deformations in the Intestine Chips compared to when cultured statically as organoids or in Transwell inserts. Infection of the intestinal epithelium with NL63 on-chip led to inflammation of the endothelium as demonstrated by loss of barrier function, increased cytokine production, and recruitment of circulating peripheral blood mononuclear cells (PMBCs). Treatment of NL63 infected chips with the approved protease inhibitor drug, nafamostat, inhibited viral entry and resulted in a reduction in both viral load and cytokine secretion, whereas remdesivir, one of the few drugs approved for COVID19 patients, was not found to be effective and it also was toxic to the endothelium. This model of intestinal infection was also used to test the effects of other drugs that have been proposed for potential repurposing against SARS-CoV-2. Taken together, these data suggest that the human Intestine Chip might be useful as a human preclinical model for studying coronavirus related pathology as well as for testing of potential anti-viral or anti-inflammatory therapeutics.

overall_design: 4 uninfected organ-on-chips (2 donors; 2 chips/donor) and 2 infected chips (1 donor). Replicate Seq-Well arrays of all chips aside from 2 uninfected chips (1 array only).

first: Andrew

last: Navia

first: Carly

last: Ziegler

last: Shalek


title: Iron accumulation and changes of cellular organelles in WDR45 mutant fibroblasts

city: Chuncheon

first: Sehyun

last: Chae

address: 1 Kangwondaehakgil

department: Division of Chemical Engineering and Bioengineering

country: South Korea

institute: Kangwon National University

summary: Iron overload in the brain, defined as excess stores of iron, is known to be related to neurological disorder. Among neurodegeneration with brain iron accumulation, we reported a specific point mutation, 977-1G>A in WDR45, showing iron accumulation in the brain, and autophagy defects in the fibroblasts. In this study, we investigated whether fibroblasts with mutated WDR45 accumulated iron, and other effects on cellular organelles. We first identified the main location of iron accumulation in the mutant fibroblasts and then investigated the effects of this accumulation on other organelles, including lipid droplets, mitochondria, and lysosomes. Ultrastructure analysis using transmission electron microscopy (TEM) and confocal microscopy showed structural changes in the organelles. Increased numbers of lipid droplets, fragmented mitochondria, and increased lysosomal vesicles with functional disorder due to WDR45 deficiency were observed. The majority of iron accumulation occurred in the lysosomal vesicles, according to correlative light and electron microscopy (CLEM). These changes were related to defects in autophagy and defective protein and organelle turnover. Gene expression profiling analysis also showed significant changes in lipid metabolism, mitochondrial function, and autophagy-related genes. Those data suggested that functional and structural changes caused impaired lipid metabolism, mitochondrial disorder, and unbalanced autophagy fluxes, due to iron overload.

overall_design: The transcriptomic profiles of patient derived WDR45 mutant fibroblasts and normal fibroblasts.

first: Ji

middle: Y

last: Mun

first: Hye

last: Lee

first: Minkyo

last: Jung


title: The effect of moderate-intensity treadmill exercise on the transcription of peripheral blood mononuclear cells in ovariectomized rats

city: Ji’nan

first: Li

last: Gao

address: No. 10600 Century Avenue, Licheng District

institute: SHANDONG SPORT UNIVERSITY

summary:
Purpose: Using RNA-sequencing technology to screen the effect of moderate-intensity treadmill exercise on the key genes that affect bone mass in the peripheral blood mononuclear cells (PBMCs) of ovariectomized (OVX) rats.
Methods: Three-month-old female Sprague–Dawley rats of Specific Pathogen Free (SPF) grade were randomly divided into the sham operation (SHAM) group, OVX group, and OVX combined exercise (OVX+EX) group. The OVX+EX group performed moderate-intensity treadmill exercise for 17 weeks. Upon completion of these exercises, the body composition and bone mineral density (BMD) were measured using dual-energy X-ray absorptiometry, and the bone microstructure of the femur was observed using micro-computed tomography scanning. PBMCs were collected from the abdominal aorta, and the differential genes were analyzed by transcriptome sequencing. The Metascape software was used for gene ontology and pathway enrichment analysis to further screen key genes.
Results: 1. In the OVX group, the body weight and body fat content were significantly higher than in the SHAM group and the body muscle content and BMD were significantly lower. 2. The trabecular bone parameters in the OVX group were significantly lower than in the SHAM group, and they were significantly higher in the OVX+EX group than in the OVX group. When compared with the SHAM group, the microstructure of the distal femur trabecular in the OVX group was severely damaged, the trabecular bones were sparse, and there was a large gap between the trabecular bones. The number and continuity of the trabecular bones were higher in OVX+EX group than in the OVX group. 3. A Venn diagram showed that there were 58 common differential genes, with a fold change ≥2 and p value <0.05. and the differential genes were mainly enriched in the PI3K-Akt signaling pathway. Five key genes were screened including CCL2, Nos3, Tgfb3, ITGb4, and LpL.
Conclusion: Moderate-intensity treadmill exercise may improve the body composition and bone mass of the OVX group by upregulating CCL2 and other genes of the PBMC. The results also showed that the PBMCs in the peripheral blood can be a useful tool for monitoring the effect of exercise on bone health in postmenopausal osteoporosis.

overall_design: the effect of moderate-intensity treadmill exercise on the mRNA profiles  in the peripheral blood mononuclear cells (PBMCs) of ovariectomized (OVX) rats.


title: Nanolipoprotein mediated Her2 protein transfection induces malignant transformation in human breast acinar cultures

city: Livermore

first: Claire

last: Robertson

address: 7000 East Ave.

institute: Lawrence Livermore National Lab

summary: We describe transcriptomic changes in HMT-3522-S1 cells cultured in the acinar morphogenesis assay in reponse to either empty-nanolipoprotein stimulus, Her2-nanolipoprotien stimulus or control unstimulated cells.

overall_design: HMT-3522-S1 nonmalignant human breast epithelial cells were cultured in laminin rich extracellular matrix hydrogels for 10 days in either control/no stimulus condition, in the presence of  5ug/ml nanolipoprotein particles comprised of His-tagged Apolipoprotein A1 and 1,2-dimyristoyl-sn-glycero-3-phosphocholine, or in the presence of 5ug/ml nanolipoprotein particles containing the above plus human full length ErbB2 protein (Her2).

first: Wei

last: He

first: Angela

last: Evans

middle: F

last: Hynes

first: Matthew

last: Coleman


title: Gene expression profiles of colorectal cancer cells grown in 2D/3D conditions

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: Gene expression analysis was performed through RNA-Sequencing on samples prepared from a panel of four CRC cell lines (HT29, HCT116, LS174T, LS513) grown in either 2D or 3D cell culture conditions. Our gene expression data reveal that more than 2000 gene expression profiles are affected by the growth conditions for each cell lines even if samples prepared from each cell line still group together. Our data also demonstrate that hierarchical clustering mostly relies on the MSS/MSI phenotypes of the CRC cells.

overall_design: Transcriptome of CRC cell lines grown in either 2D or 3D cell culture conditions

first: Clémentine

last: Dillard

first: Ammara

last: Mohammad

first: Laurent

last: Jourdren

first: Alexandre

middle: E

last: Escargueil


title: Oleil hydroxytyrosol (HTOL) exerts anti-myeloma activity by antagonizing key survival pathways in malignant plasma cells

city: Milan

first: Antonino

last: Neri

state: Milan

address: Via Francesco Sforza, 35

country: Italy

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

summary:
Polyphenols from olive oil are endowed with several biological activities. Chemical modifications have been recently applied to these compounds to improve their therapeutic activity in different pathological settings, including cancer. Herein, we describe the in vitro effects elicited by oleil hy-droxytyrosol (HTOL), a synthetic fatty ester of natural hydroxytyrosol with oleic acid, on multiple myeloma (MM) cells. HTOL reduced the viability of different human MM cell lines (HMCLs), triggering UPR, ER stress and apoptosis, while it was not cytotoxic against healthy peripheral blood mononuclear cells.
Microarray-based whole transcriptome profiling of HTOL-treated MM cells, coupled with protein expression analyses, indicates that HTOL antagonizes molecular pathways key for malignant plasma cell survival, including the undruggable IRF4-c-MYC oncogenic axis. c-MYC gain- and loss-of-function experiments indicate that HTOL anti-tumor activity was, at least in part, due to c-MYC targeting. Taken together, these findings underscore the anti-MM activity of HTOL, providing the molecular framework for further investigation of HTOL-based treatments as novel anti-cancer agents.

overall_design: JJN3 Human myeloma Cell Line (HMCL) was treated with HTOL (5.0 µM , 24h). Global transcript expression profiles of HTOL treated JJN3 were investigated in comparison to control cells. Duplicates were used for each condition.

first: Katia

last: Todoerti

first: Maria

last: Gallo Cantafio

first: Manuela

last: Oliverio

first: Giada

last: Juli

first: Carmine

last: Rocca

first: Rita

last: Citraro

first: Pierfrancesco

last: Tassone

first: Antonio

last: Procopio

first: Giovambattista

last: De Sarro

first: Giuseppe

last: Viglietto

first: Nicola

last: Amodio


title: The ethylene-auxin crosstalk regulates the postharvest fruit ripening process in apple

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

institute: University of Trento

summary: The ripening of climacteric fruits, such as apple, is represented by a series of genetically programmed events orchestrated by the action of several hormones. In this work, we investigated the existence of a hormonal crosstalk between ethylene and auxin during the post-harvest ripening of three internationally known apple cultivars: ‘Golden Deli-cious’, ‘Granny Smith’ and ‘Fuji’. The normal climacteric ripening was impaired by the exogenous application of 1-methylcyclopropene (1-MCP) that effectively affected the production of ethylene and the physiological behaviour of specific ethylene-related qual-ity traits, such as fruit texture and the production of volatile organic compounds showed a de-novo accumulation of auxin following the application of 1-MCP. The RNA-Seq wide-transcriptome analysis evidenced as the competition at the level of the ethylene re-ceptors induced a cultivar-dependent transcription re-programming. The DEGs annota-tion carried out through the KEGG database identified as most genes were assigned to the plant hormone signaling transduction category, and specifically related to auxin and ethylene. The interplay between these two hormones was further assessed through a candidate gene analysis that highlighted a specific activation of GH3 and ILL genes, en-coding key steps in the process of the auxin homeostasis mechanism. Our results showed that a compromised ethylene metabolism at the onset of the climacteric ripening in apple can stimulate, in a cultivar-dependent fashion, an initial de-novo synthesis and de-conjugation of auxin as a tentative to restore a normal ripening progression.

overall_design: RNA-seq analysis of 11 samples (Harvest, 1DAH_ctrl, 7DAH_ctrl, 14DAH_ctrl, 21DAH_ctrl; 2m_ctrl, 1DAH_1-MCP, 7DAH_1-MCP, 14DAH_1-MCP, 21DAH_1-MCP; 2m_1-MCP)

last: Busatto

first: Alice

last: Tadiello

first: Marco

last: Moretto

first: Brian

last: Farneti

first: Francesca

last: Populin

first: Urska

last: Vrhovsek

first: Mauro

last: Commisso

first: Elisa

last: Sartori

first: Paolo

last: Sonego

first: Frano

last: Biasioli

first: Guglielmo

first: Flavia

last: Guzzo

last: Fontana

first: Kristof

last: Engelen


title: SMARCA4 loss-of-function induces cisplatin resistance to activate YAP1-dependent epithelial-to-mesenchymal in triple negative breast cancer

city: GOYANG

first: JIHYUN

last: KIM

address: 323 ILSAN-RO

institute: National cancer center

summary: We report transcriptome profiling (RNA-seq) for SMARA4 knock-out to elucidate the association with cisplatin-resistance and SMARCA4 loss-of-function using triple negative breast cancer cell lines.

overall_design: RNA-seq with SMARCA4 knock-out and WT from MDA-MB-231 and MDA-MB-468 breast cancer cell lines

first: Charny

last: Park

first: Kyungtae

last: Kim


title: RNA-seq for NB4 cell line in either the absence or presence of CEBPG

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for NB4 cell line in either the absence or presence of CEBPG

overall_design: 2 NB4 samples with CEBPG presence and 2 NB4 samples with CEBPG knockdown

first: Lu

last: Jun

first: Jiang

last: You

first: Wu

last: Shuiyan


title: Identification of Two Subsets of Murine DC1 Dendritic Cells That Differ by Surface Phenotype, Gene Expression, and Function

city: Stanford

first: Pingping

last: Zheng

address: 269 Campus Drive, CCSR

department: BMT

institute: Stanford University

summary: RNAseq of Murine Dendritic Cell Subsets

overall_design: To identify subsets of murine dendritic cells, and test the ability of each subset to induce immune responses to soluble protein and peptide antigens, cell associated antigens such as tumor antigens and histocompatibility antigens, and glycolipid antigens

first: David

last: Hongo

first: Suparna

last: Dutt

first: Rahul

last: Pawar

first: Everett

last: Meyer

first: Edgar

middle: G

last: Engleman

first: Samuel

last: Strober


title: RNA-seq for MV4-11 cell line in either the absence or presence of CEBPG

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for MV4-11 cell line in either the absence or presence of CEBPG

overall_design: 2 MV4-11 samples with CEBPG presence and 2 MV4-11 samples with CEBPG knockdown


title: Targeted RNA sequencing of varicella zoster virus-infected human brain vascular adventitial fibroblasts

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

summary: Transcriptome analysis of VZV infected primary human brain vascular adventitial fibroblasts (HBVAFs)

overall_design: Mock- and VZV-infected quiescent HBVAFs were harvested at 3 days post-infection and samples lysed and analyzed by targeted RNA sequencing of the whole human transcriptome (BioSpyder TempO-Seq).

first: Bubak

last: Andrew


title: Trabecular meshwork cell-derived exosomal microRNA expression

city: Kumamoto

first: Junji

last: Saruwatari

state: Select One...

address: 5-1 Oe-honmachi, Chuo-ku

department: Department of Pharmacology and Therapeutics

institute: Kumamoto University

summary:
Trabecular meshwork cells in eyes with glaucoma aquire mesenchymal phenotypes. The types of microRNAs in exosomes may differ between static and glaucomatous status and their effects on aqueous humor regulation are still uknown.
We used microarrays to identify the differential microRNA expression related to interaction between trabecular meshwork cells and Schlemm's canal endothelial cells.

overall_design: Transcriptomic profile of microRNAs in exosomes derived from monkey trabecular meshwork cells treated with TGF-β2, collagen type 1 or those without (controls).

first: Eri

last: Takahashi

first: Tomokazu

last: Fujimoto

first: Toshihiro

last: Inoue


title: RNA-seq analysis reveals RNA expression profiles following LPS-induced inflammation in bovine mammary epithelial cells

city: Yinchuan

first: Xing-Ping

last: Wang

state: Ningxia

address: No. 489, Helan Shanxi Road, Xixia District

department: College of animal science and technology

institute: Ningxia University

summary:
Purpose: to detect expression profile of RNA (lncRNA and circRNA) and elucidate differentially expressed RNAs (DElncRNAs and DEcircRNAs) with potential roles during lipopolysaccharide (LPS)-induced inflammation models of bovine mammary epithelial cells MAC-T in vitro.
Methods: bovine mammary epithelial cells MAC-T were exposed to LPS for 0, 6 and 12 hours to assess the expression profiles of RNA (lncRNA and circRNA) using RNA-seq.
Results: totally 112 DElncRNAs and 71 DEcircRNAs were screened out at different time points. Functional enrichment analysis on target genes of lncRNAs and host genes of circRNAs indicated that these genes were involve in regulating inflammation-related signaling pathways, including Notch, NF-κB, MAPK, PI3K-Akt, mTOR, MAPK and NOD-like receptor signaling pathway.
Conclusion: these differentially expressed RNAs (DElncRNAs and DEcircRNAs) may be involved in the regulation of a variety of immune-related processes including inflammatory responses bovine mammary epithelial cells exposed to LPS via some vital signaling pathways. This study lays a foundation for further research on molecular regulation of bovine mastitis, and also provides a reference for breeding strategies based on molecular markers for mastitis resistance in dairy cows.

overall_design: Bovine mammary epithelial cells MAC-T previously frozen in liquid nitrogen were thawed and cultured in in three 6-well plates. When bovine mammary epithelial cell monolayers reached 80% confluence, one 6-well plate cells (0 hpi) were collected as the control group, and the remaining two 6-well plates were treated with 50 ng/μL LPS to stimulate an inflammatory response. The respective 6-well plates were collected at 6 and 12 hpi as the experimental groups. Subsequently, all samples were used to perform the RNA-seq.

first: Jin-Peng

first: Qi-Chao

last: Hu

first: Jian

last: Yang

first: Zhuo-Ma

last: Luoreng


title: RNA-seq for MV4-11 and NB4 cell line in either the absence or presence of CEBPG

first: Fang

last: Fang

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: mRNA-Seq analysis of cSCC cells followed by siRNA-induced gene knockdown of C1r.

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

country: Finland

institute: University of Turku

summary: Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin cancer, and its incidence is increasing globally. Chronic inflammation has been recognized as a risk factor for cSCC and inflammation is a typical feature in the progression of premalignant actinic keratosis lesions to invasive and metastatic cSCC. The complement system is an important part of innate immunity, and activation of complement is detected in the microenvironment of tumors and has been considered a host defense mechanism against cancer cells. The complement cascade can be activated via three distinct pathways, namely the classic, lectin, or alternative pathways, which all lead to activation of lytic pathway and formation of the membrane attack complex, a pore-like structure on the target cell membrane resulting in the lysis of the target cell. The classical pathway of complement is typically activated by binding of C1 complex to antibodies bound to their target antigens. The C1 complex consists of six subcomponents of C1q, each with a collagenous triple helix of subunits C1qA, C1qB, and C1qC chains and two copies of serine proteases C1r and C1s subunits each. Whole transcriptome analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=4) and oligonucleotide array-based expression analysis of cSCC cells (n=8) and normal human epidermal keratinocytes (NHEKs, n=5) revealed overexpression of C1r in cSCC cells (GSE66412 and GSE66368, respectively). Previously it has been shown that knockdown of C1r promotes apoptosis of cSCC cells and significantly suppresses growth and vascularization of human cSCC xenograft tumors in vivo (Riihilä et al. Br J Dermatol 2020; 182:658-670). In this respect, we have studied the RNA expression profile of cSCC cells after C1r knockdown.

overall_design: Total RNAs from negative control siRNA and C1r siRNA-treated cSCC cell lines (n=3) were extracted. The samples were sequenced using Illumina sequencing.

first: Kristina

last: Viiklepp

first: Veli-Matti

last: Kähäri


title: Whole-transcriptome analysis and construction of vernalization-related ceRNA-miRNA-target gene regulatory network in Chinese cabbage (Brassica campestris L. ssp. pekinensis) [seed mRNA]

city: Shenyang

first: Zhiyong

last: Liu

state: Liaoning Province

address: Dongling Road 120

institute: Shenyang Agriculral University

summary: The transition from vegetative growth to reproductive growth involves many pathways. Vernalization is crucial to the formation of floral organs, the regulation of flowering time and plant breeding. The purpose of this study was to identify the mRNA, microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) related to vernalization of Chinese cabbage, and to construct a competitive endogenous RNA (ceRNA) network, so as to provide valuable information for exploring the molecular mechanism of vernalization of Chinese cabbage.  Results: The results of whole-transcriptome sequencing showed that 2702 mRNAs, 151 lncRNAs, 16 circRNA, and 233 miRNAs were differentially expressed in vernalized (‘Ver’) and non-vernalized (‘Nor’) seeds of Chinese cabbage. Some transcription factors and regulatory proteins that play important roles in vernalization pathway have been identified, such as the transcription factors of  WRKY, MYB, NAC, bHLH, and MADS-box, zinc finger protein CONSTANS like gene and B3 domain protein. We constructed vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA-DEmRNA, 67 DEmiRNA-DElncRNA, and 12 DEmiRNA-DEcircRNA interactions in Chinese cabbage. Meanwhile, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs were identified, which were involved in the regulation of flowering time, floral organ formation, bolting and flowering.  Conclusions: The candidate differentially expressed mRNA, miRNA, lncRNA and circRNA for vernalization of Chinese cabbage were identified by the whole-transcriptome sequencing, and the ceRNA network was constructed. This study laid a foundation for further study on the molecular mechanism of vernalization in Chinese cabbage.

overall_design: we performed the whole-transcriptome sequencing on Chinese cabbage seeds that were vernalized at 4℃ for 25 days and seeds that were not vernalized, identified the expression changes of mRNA, miRNA, lncRNA, and circRNA, and carried out Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) enrichment analysis to explore their potential regulatory role.

first: Fengyan

last: Shi

first: Hezi

last: Xu


title: BACH1, the master regulator of oxidative stress, modulates CFTR gene expression

first: Ann

last: Harris

state: Ohio

address: 2109 Adelbert Rd Building

department: Genetics and Genome Sciences

institute: Case Western Reserve University

type: Genome binding/occupancy profiling by high throughput sequencing


title: Whole-transcriptome analysis and construction of vernalization-related ceRNA-miRNA-target gene regulatory network in Chinese cabbage (Brassica campestris L. ssp. pekinensis) [seed miRNA]

type: Non-coding RNA profiling by high throughput sequencing


title: BACH1, the master regulator of oxidative stress, modulates CFTR gene expression [RNA-seq]

summary: The cystic fibrosis transmembrane conductance regulator (CFTR) gene lies within a TAD in which multiple cis-regulatory elements (CREs) and transcription factors (TFs) regulate its cell-specific expression. The CREs are recruited to the gene promoter by a looping mechanism that depends upon both architectural proteins and specific TFs. An siRNA screen to identify TFs coordinating CFTR expression in airway epithelial cells suggested an activating role for BTB Domain and CNC Homolog 1 (BACH1). BACH1 is a ubiquitous master regulator of the cellular response to oxidative stress. Here we show that BACH1 may have a dual effect on CFTR expression by direct occupancy of CREs at physiological oxygen (~8%), while indirectly modulating expression under conditions of oxidative stress. Hence BACH1, can activate or repress the same gene, to fine tune expression in response to environmental cues such as cell stress. Furthermore, our 4C-seq data suggest that BACH1 can also directly regulate CFTR gene expression by modulating locus architecture through occupancy at known enhancers and structural elements, and depletion of BACH1 alters the higher order chromatin structure.

overall_design: 4 RNA-seq (single end) datasets, 2 replicates between 2 treatment groups

first: Monali

last: NandyMazumdar

first: Alekh

last: Paranjapye

first: James

last: Browne

first: Shih-Hsing

last: Leir

first: Shiyi

last: Yin


title: BACH1, the master regulator of oxidative stress, modulates CFTR gene expression [ChIP-seq]

overall_design: 2 IDR ChIPseq datasets generated from 2 replicates each

last: Brown


title: Profile of podocyte translatome during development of type 2 and type 1 diabetic nephropathy using podocyte-specific TRAP mRNA RNA-seq

city: Nashville

first: Yinqiu

last: Wang

state: TN

address: 313 Harpeth view circle

department: medicine

institute: vumc

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

overall_design:
Examination of the podocyte gene expression changes in 2 different diabetic models

Diabetes type 1 induced with STZ treatment
Diabetes type 2 occurs in genotype eNOS-/- db/db

first: Raymond


title: Genome-wide maps of FLI1 in two GCB cell lines

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

summary: FLI1 DNA binding sites have been identified in two GCB lymhoma cell lines.

overall_design: Examination of FLI1 occupancy in two GCB lymphoma cell lines.

first: Francesco

last: Bertoni

first: Giulio

last: Sartori


title: Changing and stable chromatin accessibility supports transcriptional overhaul during neural stem cell activation

city: Providence

first: Ashley

last: Webb

state: RI

address: 70 Ship St.

department: Molecular Biology, Cell Biology, and Biochemistry

institute: Brown University

summary: Adult neural stem cells are largely quiescent, and require transcriptional reprogramming to re-enter the cell cycle before neurogenesis. However, mechanisms underlying the transcriptional overhaul during NSC activation remain undefined. Here, we identify the chromatin accessibility differences between primary neural stem/progenitor cells in quiescent and activated states. These distinct cellular states exhibit shared and unique chromatin profiles, both associated with gene regulation. Interestingly, accessible chromatin states specific to activation or quiescence are active enhancers bound by pro-neurogenic and quiescence factors, ASCL1 and NFI. In contrast, shared sites are enriched for core promoter elements associated with translation and metabolism. Unexpectedly, through integrated analysis, we find that many sites that become accessible during NSC activation are linked to downregulation of gene expression and associated with pro-quiescence factors, revealing a novel mechanism that may preserve quiescence re-entry. Together, our findings reveal how accessible chromatin states regulate the transcriptional switch between NSC quiescence and activation.

overall_design: ATAC-seq and H3K4me3 ChIP-seq profiles of postnatal day 5 mouse neural stem/progenitor cells in activated and BMP4-induced quiescence conditions.

first: Sun

last: Maybury-Lewis


title: Chromatin isolation by RNA purification sequencing of LINC02015 in human aortic smooth muscle cells

status: Public on Nov 16 2021

city: Shanghai

first: Qiang

last: Ji

address: 180 Fenglin Rd.

institute: Zhongshan Hospital Fudan University

summary: This study was designed to explore the role of LINC02015 in regulating biological behaviors of vascular smooth muscle cells (VSMCs) and investigate the interacting targets of LINC02015 with high-throughput techniques and bioinformatics analysis. Chromatin isolation by RNA purification (ChIRP) sequencing was applied to explore the interaction relationship among LncRNA, RNA-binding protein and DNA. Localization of the active binding sites was specified by high-throughput sequencing with STAR2. Peak calling analysis was applied to spot enriched gene peaks with MACS.

overall_design: Examination of LINC02015 binding sites in human aortic smooth muscle cells


title: BACH1, the master regulator of oxidative stress, modulates CFTR gene expression [4C-seq]

city: Cleveland

overall_design: Analysis of the 3D chromatin architecture at the CFTR locus to determine interaction frequencies between elements which lead to changes in CFTR gene regulatory patterns upon BACH1 Knockdown.

first: Shiy


title: Endothelial cell-specific reduction of heparan sulfate suppresses glioma growth in mice

city: Gifu

first: Hiroyuki

last: Tomita

address: 1-1 Yanagido

institute: Gifu University

summary: we examined how HS-reduced vascular endothelial cells are involved in the proliferation of glioma by using mice in which Ext-1 expression is specifically suppressed in vascular endothelial cells.

overall_design: We prepared mouse glioma (GL261) cells. We transplanted the cells to wild type (WT) and Ext1 flox/flox; VE-Cre mice (N=4 each). We removed the developing tumors from mouse brain 14 to 21 days later and extracted RNA from whole tumors. Finally, we perfomred RNA microarray analysis.

first: Takamasa

last: Kinoshita


title: Genome-wide mRNA profiling of PBMCs from TB patients (TB) and healthy controls (HC)

city: Beijng

first: Fang

last: Xu

state: Beijing

address: 56 Nanlishi Road, Xicheng District

department: Beijing Pediatric Research Institute

institute: Beijing Children’s Hospital, Capital Medical University

summary: Transcriptome microarray analysis was conducted to examine the gene expression profiling of PBMCs from active TBs and HCs. All 18,853 mRNAs in the microarray were used to draw a Heatmap of differential genes according to their expression levels. The genes that exhibited significant changes in expression were used for further validation. The TB group (n=15) exhibited a significantly different profile compared to the HC (n=15) group (Fig. 1a). A total of 1,595 differentially expressed mRNAs were identified between the two groups. Of these, 335 mRNAs were up-regulated (fold change ≥ 2), and 1,260 mRNAs were down-regulated (fold change ≥ 2).

overall_design: RNA samples from each group were used to generate fluorescence labeled cRNA targets for the Agilent Whole Human Genome Oligo Microarray (4 × 44 K, including ~41,000 genes and transcripts). Labeled cRNA targets were then hybridized with the slides. After hybridization, slides were scanned on the Agilent Microarray Scanner (Agilent Technologies). Data were extracted with Feature Extraction software 10.7 (Agilent Technologies). Raw data were normalized by Quantile algorithm, Gene Spring Software 12.6.1 (Agilent Technologies). The microarray experiments were performed by following the protocol of Agilent Technologies at Shanghai Biotechnology Corporation. A total of 1,595 differentially expressed mRNAs were identified between the two groups.

first: Hui

last: Qi

first: Lin

last: Sun

first: Adong

last: Shen


title: Differential gene expression analysis of pbl19/pPBL19C3A-GFP-HA transgenic plants

city: Guangzhou

first: yujia

last: Li

address: No. 132, Huan East Road, Panyu District, Guangzhou City

department: School of life science

institute: sun yet-sen university

summary:
Purpose: RNA-seq analysis of the pbl19/pPBL19:PBL19C3A-GFP-HA, sid2pbl19/pPBL19:PBL19C3A-GFP-HA and eds1pbl19/pPBL19:PBL19C3A-GFP-HA plants and identified a large number of differentially expressed genes in these plants relative to wild-type plants.
Methods: For RNA-seq analyses, a total amount of 1 mg RNA per sample was used for RNA-seq library construction.
Results: RNA-seq analysis of wild type(WT), pbl19/pPBL19:PBL19C3A-GFP-HA, sid2pbl19/pPBL19:PBL19C3A-GFP-HA and eds1pbl19/pPBL19:PBL19C3A-GFP-HA at 28 DAG.Numbers of differentially expressed genes in pbl19/pPBL19::PBL19C3A-GFP-HA plants compared to WT.1981 differentially expressed genes were constantly up-regulated in pbl19/pPBL19::PBL19C3A-GFP-HA plants compared to WT
Conclusions: Receptor-like cytoplasmic kinase PBL19 exhibited the highest transcriptional upregulation among the forty-six genes of the RLCK VII subfamily in pbl19/pPBL19C3A-GFP-HA and sid2 pbl19/pPBL19C3A-GFP-HA transgenic plants.eds1 pbl19/pPBL19:PBL19C3A-GFP-HA plants were fully restored to a wild-type(WT) appearance

overall_design: mRNA  of 28-day old wild type (WT) and pbl19/pPBL19C3A-GFP-HA, sid2pbl19/pPBL19:PBL19C3A-GFP-HA and eds1pbl19/pPBL19:PBL19C3A-GFP-HA transgenic plants, total 8 samples were analyzed, one biological replicate were conducted in this experiment. WT as a control.

first: jiao

last: Xue


title: Single-cell transcriptomic profiles reveal changes associated with BCG-induced trained immunity and protective effects in circulating monocytes

city: Cambridge

first: Lingjia

last: Kong

state: MA

address: 415 Main St.

department: Infectious Disease and Microbiome

institute: Broad Institute

summary: Bacillus Calmette-Guérin (BCG) vaccine is one of the most widely-used vaccines worldwide. In addition to protection against tuberculosis, BCG confers a degree of non-specific protection against other infections by enhancing secondary immune responses to heterologous pathogens, an effect termed trained immunity. To better understand BCG-induced immune reprogramming, we performed single-cell transcriptomic measurements before and after BCG vaccination using secondary immune stimulation with bacterial lipopolysaccharide (LPS). We find that BCG vaccination reduces systemic inflammation, and we identify 75 genes with an altered response to LPS, including several inflammatory mediators such as CCL3 and CCL4 which have a heightened response. Co-expression analysis reveals gene modules containing these cytokines lose coordination after BCG vaccination. Others have increased coordination, including several humanin nuclear isoforms which we confirmed induce trained immunity in vitro. Our results link in vivo BCG administration to single cell transcriptomic changes, validated in human genetics experiments, and highlight new genes which may be responsible for the non-specific protective effects of BCG.

overall_design: Single cell RNA-seq of monocytes from 3 healthy donors during 3 visits. On the first visit, blood collection was performed before BCG vaccination. Follow-up samples were collected 2 weeks and 3 months after the initial visit

first: Simone

last: Moorlag

first: Ariel

last: Lefkovith

first: Bihua

first: Vasiliki

last: Matzaraki

first: Mihai

last: Netea

first: Ramnik

last: Xavier


title: Dietary palmitic acid promotes a prometastatic memory based on Schwann Cell activation

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

summary: Metastasis is promoted by fatty acid (FA) uptake and metabolism 1-2 . How this works, or whether all dietary FAs are prometastatic, is not known. Here we show that dietary palmitic acid (PA), but not oleic acid (OA) or linoleic acid, promotes metastasis in oral carcinomas and melanoma, indicating specificity of action for distinct FAs. Strikingly, tumours acutely exposed to a PA–rich diet remain highly metastatic even when serially transplanted. This PA–induced prometastatic memory requires the FA transporter CD36 as well as the epigenetically stable deposition of histone H3 lysine 4 trimethylation by the methyltransferase Set1A/COMPASS. Bulk, single cell and positional RNA sequencing indicate that genes with this metastatic memory predominantly relate to a neural  signature that stimulates activation of intratumor Schwann cells and perineural invasion, two parameters strongly correlated with metastasis but etiologically poorly understood 3-4 . Mechanistically, tumour-associated Schwann cells secrete a specialized pro-regenerative extracellular matrix reminiscent of perineuronal nets, which when ablated strongly inhibits metastatic colonization. The induction of the epigenetic neural signature and its associated long-term boost in metastasis downstream of PA require the transcription factor EGR2 and the glial cell-stimulating peptide galanin. We provide evidence for a long-term epigenetic stimulation of metastasis by a dietary metabolite related to a pro-regenerative state of tumour-activated Schwann cells. In addition to underscoring the potential danger of eating large amounts of PA, our results reveal novel epigenetic and neural-related therapeutic strategies for metastasis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA sequencing and Visium Spatial Transcriptomics was used to explore changes in the tumor microenvironment in response to a fatty acid rich diet. Samples from mouse models under control and palmitic acid rich diets in control and CD36 knockouts.

first: Marc

last: Bayes

first: Gloria

middle: P

last: Angulo

first: Salvador

middle: A

last: Benitah

first: Holger

last: Heyn


title: Molecular basis of BMP-responsiveness switching during neural development

city: Fukuoka

first: Sayako

last: Katada

address: Higashiku Maidashi

institute: Kyushu University

summary: Bone morphogenetic proteins induce neuronal and astrocytic differentiation in mid-gestational (e.g. E11+2DIV), and late-gestational (e.g. E14+5DIV) neural stem cells (NSCs), respectively. We found that Smads, downstream transcription factors of BMP signaling, target dramatically different genomic regions in the neurogenic and gliogenic NSCs. The purpose of this study is to understand histone H3K27 tri-methylation profiles around Smads-binding sites in neurogenic and gliogenic NSCs, and uncover the mechanisms underlying distinct effects of BMPs on developmentally different NSCs.  We found that histone H3K27 tri-methylation around Smads binding sites quickly change as gestation proceeds, strongly associated with the alteration of accessibility of Smads to the regions.

overall_design: Examination of histone H3K27me3 profiles in E11 or E14 derived NSCs (2 replicates) and IgG as negative control.

first: Kinichi

last: Nakashima


title: Astrocytes Tet1 regulates neuronal  development and cognition through  modulating GluA1

city: hangzhou

first: wenzheng

last: qu

address: Kaixuan Road

institute: Zhejiang University

summary: Using RNA sequencing, we found that Tet1 alters gene expression. Mechanistically, we found that Tet1 deficiency leads to the abnormal Ca2+ signaling by regulating the expression of GluA1, which can be rescued by ectectopic expression of GluA1. Collectively, our findings suggest that Tet1 plays important functions by regulating astrocytes Ca2+ signaling.

overall_design: Astrocytes were isolated from two P1 Tet1 WT or KO mice and cultured in a PDL-coated T25 flask for about 7 days.

first: Weize

last: Xu

first: Xuekun


title: Transcriptomic Mapping for Human Parotid Gland at Single-Cell Resolution

city: Chengdu

first: Weimin

last: Lin

state: Sichuan

address: Wuhou strict, People South Street

institute: Sichuan University

summary: As the largest salivary gland in oral cavity, the parotid gland plays an important role in initial digesting and lubricating food. The abnormal secretory function of parotid gland can lead to dental caries and oral mucosal inflammation. In recent years, single-cell RNA sequencing (scRNA-seq) has been used to explore the heterogeneity and diversity of cells in various organs and tissues. However, the transcription profile of human parotid gland at single-cell resolution has not been reported yet. In this study, we constructed the cell atlas of human parotid gland using 10x Genomics platform. Characteristic gene analysis identified the biological functions of serous acinar cell populations in secreting digestive enzymes and antibacterial proteins. We revealed the specificity and similarity of parotid gland comparing to other digestive glands through comparative analyses of other published scRNA-seq datasets. We also identified the cell-specific expression of hub genes for Sjogren’s syndrome in human parotid gland by integrating the results of GWAS and bulk RNA-seq, which highlighted the importance of immune cell dysfunction in parotid Sjogren’s syndrome pathogenesis.

overall_design: After the parotid gland sample was obtained, it was stored in tissue preservation solution (Miltenyi) at 4℃ and transferred to the laboratory. To obtain a qualified single-cell suspension, the parotid gland tissue was cut into small pieces of 1 mm3, and digested in collagenase (1mg/mL) and dispase (1 mg/mL) by shaking of 200 rpm at 37°C for 45 minutes. Dead cell removal magnetic beads (Miltenyi) were used to remove dead cells and cell debris. The cell suspension was centrifuged and resuspended in Ca2+ and, Mg2+ free PBS to reach a cell concentration of 900-1500cell/μL. Approximately 20,000 cells were loaded. cDNA library was constructed using 10x Chromium single cell v3.1 reagent, and sequenced on the Illumina Nova-seq system.

first: Miao

last: Chen


title: Comparison of gene expression signatures in pancreatic islets and pathogenic T lymphocytes from sublines of non-obese diabetic (NOD) mice

city: Dallas

first: Eva Marie

last: Moresco

state: TX

address: 5323 Harry Hines Boulevard

department: Center for the Genetics of Host Defense

institute: University of Texas Southwestern Medical Center

summary: To gain further insight into potential specific gene signatures expressed by pancreatic islet cells and pathogenic CD4+ T lymphocytes isolated from sublines of non-obese diabetic (NOD) mice expressing high or low autoimmune (type 1) diabetes incidence.

overall_design: Gene expression was measured in purified islets of Langerhans and CD4+ pathogenic T lymphocytes from non-obese diabetic (NOD) mice expressing high (NOD/NckH) or low (NOD/NckL) autoimmune (type 1) diabetes incidence. Five independent samples of each experimental tissue (pancreatic islets from 3 week/old mice), CD4+ pathogenic spleen T cells from 6 and 15 week/old mice) isolated from NOD/NckH or NOD/NckL male mice were analyzed.

first: Chatenoud

last: Lucienne

first: Hildebrand

last: Sara


title: A multifunctional locus controls motor neuron differentiation through short and long non coding RNAs

city: Rome

first: Irene

last: Bozzoni

address: Piazzale Aldo Moro 5

department: Biology and Biotechnologies "Charles Darwin"

institute: Sapienza University of Rome

summary: The transition from dividing progenitors into post-mitotic motor neurons is orchestrated by a series of events mainly studied at the transcriptional level by analyzing the activity of specific programming transcription factors. In this work, we describe that a motor neuron-specific transcriptional unit, harboring a lncRNA (lncMN2-203) and two miRNAs (miR-325-3p and miR-384-5p), controls such transition at the post-transcriptional level. Through the use of in vitro differentiation of mESC and single-cell sequencing of CRISPR/Cas9 mutants, we demonstrate that lncMN2-203 affects motor neuron differentiation by sponging miR-466i-5p and up-regulating its targets; among them Onecut2, which is the upstream regulator of the MN-specific programming factor Islet-1. In synergy with lncMN2-203, instead the depletion of the co-transcribed miR-325-3p and miR-384-5p was found to mainly sustain proliferation-related factors. These findings indicate the functional relevance of the MN2 locus and contribute to elucidate additional layers of regulation controlling the specificity of motor neuron differentiation.

overall_design: CRISPR/Cas9 gene editing approach was applied to generate loss-of-function mutant mESCs of MN2 locus (DeltaSP and KO). Control (WT) and mutants cells were differentiated to Embroyd Bodies at day6 (EB6) according to MN differentiation protocol published in Wichterle and Peljto, 2008. For each condition two clones were analyzed with single cell RNA sequencing (10X Genomics Chromium, Chromium Single Cell 3’ Solution V3). FASTQ reads were aligned, filtered and counted through the Cell Ranger pipeline (v4.0) using standard parameters. The Mm10 genome version was used in alignment step and annotation refers to Ensembl Release93. See methods for more details.

first: Andrea

last: Carvelli

first: Adriano

last: Setti

first: Fabio

last: Desideri

first: Silvia

last: Galfrè

last: Biscarini

first: Tiziana

last: Santini

first: Alessio

last: Colantoni

first: Giovanna

last: Peruzzi

first: Matteo

last: Marzi

first: Davide

last: Capauto

last: Di Angelantonio

first: Monica

last: Ballarino

first: Francesco

last: Nicassio

first: Pietro

last: Laneve


title: H3K4me3 in vitro ChIP-Sequencing data [EGR2 KD]

first: Antoni

last: Berenguer-LLergo

summary: H3K4me3 profiling of OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal.

overall_design: Untreated and post 14 days PA treatment in SCC-25 EGR2 KD

first: Carmelo

last: Laudanna

first: Diana

last: Dominguez


title: EGR2 in vitro ChIP-Sequencing data [SCC-25 (pLKO.1)]

summary: EGR2 profiling of OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal.

overall_design: Untreated and post 14 days PA treatment in SCC-25 (pLKO.1)

last: Domínguez

first: Inmaculada

last: Hernández


title: RNA sequencing from in vitro cultured OSCC cells

summary: Transcriptominc profiling of OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal.

overall_design: Untreated and post 14 days PA treatment in SCC-25


title: EGR2 in vitro ChIP-Sequencing data [SCC-25 CD36_KD]

overall_design: Untreated and post 14 days PA treatment in SCC-25 CD36_KD


title: H3K9me3 in vitro ChIP-Sequencing data [SCC-25]

summary: H3K9me3 profiling of OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal.


title: MapToCleave: high-throughput profiling of microRNA biogenesis in living cells

city: Solna

first: Wenjing

last: Kang

address: SciLifeLab, Tomtebodavägen 23

country: Sweden

institute: SciLifeLab

summary: We here introduce MapToCleave, a new method to simultaneously profile processing of thousands of distinct RNA structures in living cells. We find that miRNA precursors connected to a stable lower basal stem are more efficiently processed and also have higher expression in vivo in tissues from twenty animal species. We systematically compare the importance of known and novel sequence and structural features, and test miRNA precursors from ten animal and plant species in human cells. Last, we provide evidence that the known GHG motif better predicts processing when defined as a structure rather than sequence motif, consistent with recent cryo-EM studies. In summary, we apply a new screening assay in living cells to reveal the importance of lower basal stem stability for miRNA processing and in vivo expression.

sample_organism:
Homo sapiens
Mus musculus
synthetic construct

overall_design: Two major experiments are included: 1) MapToCleave assay, where we applied in a single experiment to simultaneously profile the processing of 12,472 distinct RNA structures in living cells. These structures include bona fide human microRNA precursors, non-human microRNA precursors and control non-hairpin sequences. First, the test sequences were synthesized and cloned into an expression vector. The generated expression constructs were pooled in a single library and then transfected into human HEK-293T and HeLa cells and mouse NIH-3T3 and MEF cells. The successfully transfected individual vectors were identified by DNA sequencing. The test sequences were transiently expressed and the ones forming the correct hairpin structure were processed into small RNAs, which were captured by small RNA sequencing. Here we provide small RNA sequence data from HEK-293T mock cells, HEK-293T cells transfected with one time (1x) of the concentration of MapToCleave library, HEK-293T cells transfected with ten times (10x) of the concentration of MapToCleave library, HeLa mock cells, HeLa cells transfected with MapToCleave library, NIH-3T3 mock cells, NIH-3T3 cells transfected with 1x of MapToCleave library, MEF mock cells and MEF cells transfected with 1x of MapToCleave library. We provide DNA sequencing data from HEK-293T cells transfected with 1x of MapToCleave library and NIH-3T3 cells transfected with 1x of MapToCleave library. 2) Experimental validation of stability of lower basal stem tuning of microRNA processing, where we tested the processing of four variants of mir-16, one of which should stabilize the lower basal stem and improve processing (hsa-mir-16-1 variant 1) and three of which should destabilize the lower basal stem and impair processing (hsa-mir-16-1 variant 2-4). In each experiment we co-transfected with equimolar abundances of mir-30a and mir-125a for normalization, and all transfected miRNAs were additionally modified (tagged) in the mature region to discern them from endogenous miRNAs. We also tested the processing of three variants of mir-30a, two of which should stabilize the lower basal stem and improve processing (hsa-mir-30a variant 1-2) and one of which should destabilize the lower basal stem and impair processing (hsa-mir-30a variant 3). In each experiment we co-transfected with equimolar abundances of mir-16 and mir-125a for normalization, and all transfected miRNAs were additionally modified (tagged) in the mature region to discern them from endogenous miRNAs.

first: Bastian

last: Fromm

first: Anna

last: Houben

first: Eirik

last: Høye

first: Daniela

last: Bezdan

first: Carme

last: Arnan

first: Kim

last: Thrane

first: Michaela

last: Asp

first: Rory

middle: B

last: Johnson

first: Inna

last: Biryukova

first: Marc

last: Friedländer


title: H3K4me1in vitro ChIP-Sequencing data [H3K4me1_PA_SCC25_VDH15]

summary: H3K4me1 profiling of OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal.

overall_design:
H3K4me1 ChIPs for Untreated and post 14 days palmitic acid (PA)-treated SCC-25 and VDH-15 cells were performed in biological triplicates. The aim of this data set was to determine whether H3K4me1 displayed different ChIP profiles 14 days post PA stimulation when compared to the control Untreated condition (control pLKO.1); allowing us to characterize the long-term effects of PA stimulation in the H3K4me1 profile of our cells.
Please note that the 'input DNA_SCC-25' (GSM4489073) is duplicated sample record of GSM4489060 for the convenient retrieval of the complete raw data from SRA as it was re-used.

first: Salvador

last: Aznar


title: H3K4me3 in vitro ChIP-Sequencing data [H3K4me3_PA_SCC25]

last: Berenguer-LLergo

overall_design:
H3K4me3 ChIPs for Untreated and post 14 days palmitic acid (PA)-treated SCC-25 cells were performed in biological triplicates. The aim of this data set was to determine whether H3K4me3 displayed different ChIP profiles 14 days post PA stimulation when compared to the control Untreated condition (control pLKO.1 cells); therefore allowing us to characterize the long-term effects of PA stimulation in the H3K4me3 profile of our cells.
Please note that the 'input DNA_SCC-25' (GSM4489095) is duplicated sample record of GSM4489060 for the convenient retrieval of the complete raw data from SRA as it was re-used.


title: H3K4me3 in vitro ChIP-Sequencing data [H3K4me3_OA_SCC25_VDH15]

summary: H3K4me3 profiling of OSCC cells following in vitro exposure to oleic (OA) for 4 days and after 14 days of palmitic acid withdrawal.

overall_design: Please note that the 'input DNA' (GSM4489087, GSM4489088) is duplicated sample record of GSM4489060 and GSM4489074, respectively, for the convenient retrieval of the complete raw data from SRAas it was re-used.


title: A multi-omics study of bacterial growth arrest in a synthetic biology application

city: Toulouse

first: Delphine

last: Labourdette

address: Hall Gilbert Durand - Bio5 - 135 Avenue de Rangueil

department: LISBP

institute: INSA

summary: Scaling up the functioning of synthetic circuits from microplates to bioreactors is far from trivial to achieve. We here test the scalability performance of a previously developed growth switch for increasing product yields in bacteria, based on external control of RNA polymerase expression. We show that, in liter-scale bioreactors operating in fed-batch mode, growth-arrested Escherichia coli cells are able to convert glucose to glycerol at an increased yield. A multi-omics quantification of the physiology of the cells shows that apart from acetate production, few metabolic side-effects occur, while a number of specific responses to growth slow-down and growth arrest are launched on the transcriptional level. These responses include the downregulation of genes involved in growth-associated processes, such as amino acid and nucleotide metabolism and translation, and the upregulation of a heat response. Interestingly, these transcriptional responses are buffered on the proteomic level, probably due to the strong decrease of the total mRNA concentration after the diminution of transcriptional activity and the absence of growth dilution of proteins. This transforms the growth-arrested cells into “bags of proteins“ with a functioning metabolism. More generally, the analysis shows that physiological characterization of bacterial cells hosting a synthetic circuit may reveal complex patterns of adaptation on different time-scales, dynamically interacting with the bioreactor environment.

overall_design: mRNA profiles of E. coli wild-type and growth-arrested cells carrying a plasmid for glycerol production (W-gly vs R-gly)

first: D

first: H

last: de Jong


title: Henderson omalizumab study

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

summary: A considerable proportion of patients with H1-antihistamine-resistant chronic spontaneous urticaria (CSU) fails to respond to omalizumab. However, there is yet no available biomarker that accurately predicts such a response outcome.  The utility of blood basophil and eosinophil levels and exosomal and basophil micro(mi)RNAs as biomarkers of response to omalizumab in CSU was explored. In this prospective cohort study of twenty patients with antihistamine-resistant CSU, subjects were treated with 3-monthly doses of omalizumab, and their response assessed using the weekly urticaria activity score (UAS7) for a period of 12-weeks. Basophil and eosinophil levels in the blood and differentially expressed exosomal and basophil miRNAs of complete responders compared to non-responders were identified at baseline.  Canonical pathways, altered by differentially expressed miRNAs, were identified using Ingenuity Pathway Analysis (IPA). Complete responders had higher baseline basophil levels (≥21 cells/L) in the peripheral blood compared to non-responders (P = 0.005). Baseline levels of eosinophils did not differ between the study groups. Complete responders in comparison to non-responders had an expression profile characterized by a significantly higher expression of six exosomal miRNAs (miR-6499-5p, miR-7848, miR-4494-3p, miR-450a-2-3p, miR-6877-3p, and miR-3976) and lower expression of miR-141-3p. Complete responders also had higher expression of three basophil miRNAs (miR-1200, miR-1236-3p, and miR-4496). The exosomal miRNA expression profile was predicted by IPA to alter Tec Kinase Signaling pathway activity (P = 0.003).

overall_design: This was a single center, prospective cohort study, to investigate biomarkers of response to omalizumab in 22 adult patients (≥18 years) with CSU who had remained symptomatic despite the use of high dose H1-antihistamines (ClinicalTrials.gov ID: NCT02814630). The study protocol was approved by the Western Institutional Review Board. The clinical part of the study was conducted at ASTHMA Inc. Clinical Research Center, Seattle, WA  (now named Seattle Allergy & Asthma Research Institute; https://seattleallergy.org). Before inclusion in the study, all patients provided written informed consent. Inclusion criteria were: 1) at least 6 weeks of CSU with itching despite current use of up to x4 H1-antihistamines49 and 2) an urticaria activity score (UAS) during a 7-day period (UAS7) of  ≥16 (on a scale ranging from 0 to 42, with higher scores indicating greater activity)50 during the 7 days before the first treatment with omalizumab. Exclusion criteria were: 1) a clearly defined underlying cause for chronic urticaria, 2) routine administration (i.e., daily or every other day for ≥5 consecutive days) of systemic glucocorticoids, hydroxychloroquine, methotrexate, cyclosporine, cyclophosphamide, or intravenous immune globulin within the previous 30 days, 3) the use of any H2-antihistamine or leukotriene-receptor antagonist within 7 days preceding the screening visit, 4) treatment with omalizumab within the previous year, or a known hypersensitivity to omalizumab, 5) a history of cancer, or 6) women who were pregnant or nursing or unable to use an effective method of contraception during dosing with omalizumab. After initial screening within two weeks of study start, patients received one subcutaneous injection of omalizumab (Xolair®; Genentech, South San Francisco, CA) at a dose of 300 mg on Days 0, 30, and 60 (Figure 1A).  This dose was based on results of two international, multicenter, randomized, double-blind, placebo-controlled Phase 3 studies, ASTERIA I25 and ASTERIA II17 that demonstrated that omalizumab significantly decreased clinical symptoms and signs of chronic urticaria in patients who had remained symptomatic despite the use of H1-antihistamines.25 Patients were closely monitored for 2 hours after each dose of omalizumab with epinephrine administered if evidence of anaphylaxis per the joint task force guidelines of the American Academy of Allergy, Asthma & Immunology and the American College of Allergy, Asthma & Immunology. Patients were provided with an epinephrine injector for self-administration of epinephrine if development of anaphylaxis after discharge from the CRC.  Plasma samples were collected at baseline (Day 0, prior to omalizumab injection) for isolation of basophils and exosomes (Figure 1A). Patients completed a twice-daily diary that was used to determine UAS7. Patients were classified as complete responder, partial responder or non-responder based on their UAS7 score.

first: Taha

last: Al-Shaikhly

first: Theo

middle: K

last: Bammler

first: Matthew

middle: C

last: Altman

first: Andrew

last: Ayars

first: Daniel

last: Petroni

first: Stephen

last: Tilles

first: William

last: Henderson


title: H3K4me3 in vitro ChIP-Sequencing data [H3K4me3_PLKO_Set1AKD_PA_VDH15]

first: Antoni

summary: H3K4me3 profiling of control pLKO.1 and Set1A KD OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal.

overall_design:
H3K4me3 ChIPs of Untreated and post 14 days palmitic acid (PA)-treated VDH-15 cells were performed in biological triplicates (control pLKO.1 and Set1A KD cells). The aim of this data set was to determine whether H3K4me3 displayed different ChIP profiles 14 days post PA stimulation when compared to the control Untreated condition (control pLKO.1 cells). Also, Set1A knock down (KD) cells were assessed for genome wide  long-term chromatin changes induced by a short exposure to PA; allowing us to compare differences in long-term H3K4me3 changes between control pLKO.1 and Set1A KD cells upon PA stimulation and to characterize the role of the Set1A methyltransferase in such H3K4me3 PA-induced changes.
Please note that the 'input DNA_VDH15' (GSM4489108) is duplicated sample record of GSM4489074 for the convenient retrieval of the complete raw data from SRA as it was re-used.

first: Diana

last: Domínguez

first: Inmaculada

last: Hernández


title: H3K27me3 in vitro ChIP-Sequencing data [H3K27me3_PA_SCC25]

summary: H3K27me3 profiling of OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal.

overall_design: H3K27me3 ChIPs for Untreated and post 14 days palmitic acid (PA)-treated SCC-25 cells were performed in biological triplicates (control pLKO.1 cells). The aim of this data set was to determine whether H3K27me3 displayed different ChIP profiles 14 days post PA stimulation when compared to the control Untreated condition; therefore allowing to assess genome wide the long-term changes in Polycomb-repressed regions in our cells upon PA exposure.


title: H3K27ac in vitro ChIP-Sequencing data [SCC-25]

summary: H3K27ac profiling of OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal.

first: Carmelo

last: Laudanna


title: Dietary palmitic acid promotes a prometastatic epigenetic memory related to tumor innervation [III]

summary: Metastasis is promoted by fatty acid (FA) uptake and metabolism1-2. How this works, or whether all dietary FAs are prometastatic, is not known. Here we show that dietary palmitic acid (PA), but not oleic acid (OA) or linoleic acid, promotes metastasis, indicating specificity of action for distinct FAs. Strikingly, tumours acutely exposed to a PA–rich diet remain highly metastatic even when serially transplanted. This PA–induced prometastatic memory requires the FA transporter CD36 as well as the epigenetically stable deposition of histone H3 lysine 4 trimethylation by the methyltransferase Set1A/COMPASS. Genes with this metastatic memory predominantly relate to a neural signature that stimulates intratumor oligodendrogenesis and perineural invasion, two parameters strongly correlated with metastasis but etiologically poorly understood3-4. Mechanistically, induction of the epigenetic neural signature and its associated long-term boost in metastasis downstream of PA require the transcription factor EGR2 and the oligodendrocyte-stimulating peptide galanin. We provide evidence for a long-term epigenetic stimulation of metastasis by a dietary metabolite related to tumor innervation. In addition to underscoring the potential danger of eating large amounts of PA (and perhaps other saturated fats), our results reveal novel epigenetic and neural-related therapeutic strategies for metastasis.

overall_design: WT PLKO/WT PALM, Control  (2 biological x 3 technical replicates); shEGR2,shGAL Palm, Control  (3 technicalreplicates); FACS sorted CD36-bright and CD36-dim cells from non-targeting shRNA (PLKO) and short heirpin silenced EGR2 (shEGR2) and GAL (shGAL)) orthotopic oral tumor xenografts exposed to palmitic acid (PA)-rich or control diet

last: Aznar-Benitah


title: Dietary palmitic acid promotes a prometastatic epigenetic memory related to tumor innervation [IV]

overall_design: 3 biological replicates (2xVDH15 , 1xSCC25) with 3-4  techniclal replicates; FACS sorted CD36-bright and CD36-dim cells from non-targeting shRNA (PLKO) and short heirpin silenced CD36 (shCD36) orthotopic oral and melanoma tumor xenografts exposed to palmitic acid (PA)-rich, high-oleic acid (OA)-rich or control diet


title: Precision nuclear run-on sequencing (PRO-Seq) data

summary: PRO-seq profiling of OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal.

overall_design: Untreated and post 14 days PA treatment in SCC-25 cells.

first: Felipe

last: Beckedorff


title: scRNA.Sequencing data [scRNA_Seq_SCC25]

summary: Transcriptional profiling of OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal from the culture.

overall_design: single cell transcriptional profiling of CD44+ Live (Dapi-) i) 4 days untreated and 4 days palmitic acid (PA)-treated SCC-25 cells as well as ii) 14 days untreated and post 14 days PA treatment  SCC-25 cells

first: Holger

last: Heyn

first: Salvador

last: Aznar


title: MLL1 and MLL2 in vitro ChIP-Sequencing data [MLL1_MLL2_PA_VDH15]

last: Berenguer-LLergo

summary: MLL1 and MLL2 profiling of OSCC cells following in vitro exposure to palmitic acid (PA) for 4 days and after 14 days of palmitic acid withdrawal.

overall_design:
MLL1 and MLL2 ChIPs for Untreated and post 14 days palmitic acid (PA)-treated VDH-15 cells were performed in biological triplicates (control pLKO.1). The aim of this data set was to determine whether MLL1 and/or MLL2 methyltransferases displayed different ChIP profiles 14 days post PA stimulation when compared to the control Untreated condition; allowing us to interrogate their role in the H3K4me3 PA-induced changes reported in our study.
Please note that the 'input DNA_VDH15' (GSM4489132) is duplicated sample record of GSM4489074 for the convenient retrieval of the complete raw data from SRA as it was re-used.


title: Dietary palmitic acid promotes a prometastatic epigenetic memory related to tumor innervation [I]

overall_design: 3 biological replicates (2xVDH15 , 1xSCC25) with 3-4  techniclal replicates; Neural fraction cells from stroma derived from non-targeting shRNA (PLKO) and short heirpin silenced CD36 (shCD36) orthotopic oral tumor xenografts exposed to palmitic acid (PA)-rich, high-oleic acid (OA)-rich or control diet


title: Dietary palmitic acid promotes a prometastatic epigenetic memory related to tumor innervation [II]

overall_design: 3 technical replicates,  2xshRNA EGR2, 1xshRNAGAL; Neural fraction cells from stroma derived from non-targeting shRNA (PLKO) and short heirpin silenced EGR2 (shEGR2) and GAL (shGAL) orthotopic oral tumor xenografts exposed to palmitic acid (PA)-rich or control diet


title: Gene expression profiles of SCLC cells treated with KIX domain-blockade

status: Public on Nov 15 2021

city: Charlottesville

first: Kwon

last: Park

state: VA

address: 1340 Jefferson Park Ave., Pinn Hall 7039

department: Microbiology, Immunology, & Cancer Biology

institute: University of Virginia School of Medicine

summary: This comparision is to determine a global change in gene expression influenced by blocking the CREBBP/EP300 KIX domain-protein interactions with MYB-MLL fusion peptides

overall_design: M/M-WT vs M/M-51

first: Kwon-Sik

first: Kee-Beom

last: Kim